Central Heating question

I have 3 radiators that are not heating properly. I ran the system though with some cleaner fluid. I have taken them off and flshed them with a pressure washer. I have checked the valves. Still having the problem, I then turned off all the other radiators, and ran the boiler. I then drained the system and the water was dirty, so i guessed that theer was still stuf in the pipes. I refilled, ran the system (still on the 3 rads) and drained again. I repeated this several times. I then ran a hose from the the drain tap to outside and turned on the filling loop. Now, heres my question. The water at this stage runs clear, even if it is still running at pressure through the system. If I repeat my refill-run-drain process as before, the water comes out a reddish colour.
Is it the case that water running through the system (3 rads still) is missing the dirt in the pipes, or is it the fact that the water is not going through the boiler and being heated that it is not coming out a reddish colour. I am going to be replacing my boiler soon, and dont want to fit it with dirty stuff in the pipes, but dont want to be flushing my pipes continuously if the boiler is the problem. Thanks in advance.
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